X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=0a9d35f8fc85d0371429094decc40f4d36aac059;hb=80b889f0cca49103e1b20ed806755a0719789906;hp=de67c2390f0393f5488c26f6ed3929020d66e007;hpb=ad6e0dcf682399eb8b7a0ac49d3fcc63f4f991f2;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index de67c23..0a9d35f 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -20,21 +20,6 @@ */ package jalview.gui; -import jalview.analysis.AlignSeq; -import jalview.analysis.AlignmentUtils; -import jalview.datamodel.Alignment; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.Annotation; -import jalview.datamodel.HiddenColumns; -import jalview.datamodel.Sequence; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.io.FileFormat; -import jalview.io.FormatAdapter; -import jalview.util.Comparison; -import jalview.util.MessageManager; -import jalview.util.Platform; - import java.awt.Color; import java.awt.Cursor; import java.awt.Dimension; @@ -51,9 +36,11 @@ import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.awt.geom.AffineTransform; +import java.io.IOException; import java.util.Arrays; import java.util.Collections; import java.util.Iterator; +import java.util.Locale; import javax.swing.JCheckBoxMenuItem; import javax.swing.JMenuItem; @@ -62,6 +49,26 @@ import javax.swing.JPopupMenu; import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; +import jalview.analysis.AlignSeq; +import jalview.analysis.AlignmentUtils; +import jalview.bin.Console; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; +import jalview.datamodel.ContactMatrixI; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.FormatAdapter; +import jalview.io.NewickFile; +import jalview.util.Comparison; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.ws.datamodel.alphafold.PAEContactMatrix; + /** * The panel that holds the labels for alignment annotations, providing * tooltips, context menus, drag to reorder rows, and drag to adjust panel @@ -135,6 +142,7 @@ public class AnnotationLabels extends JPanel */ public AnnotationLabels(AlignmentPanel ap) { + this.ap = ap; av = ap.av; ToolTipManager.sharedInstance().registerComponent(this); @@ -208,41 +216,33 @@ public class AnnotationLabels extends JPanel AlignmentAnnotation[] aa = ap.av.getAlignment() .getAlignmentAnnotation(); - boolean fullRepaint = false; - if (evt.getActionCommand().equals(ADDNEW)) + String action = evt.getActionCommand(); + if (ADDNEW.equals(action)) { + /* + * non-returning dialog + */ AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null, null, new Annotation[ap.av.getAlignment().getWidth()]); - - if (!editLabelDescription(newAnnotation)) - { - return; - } - - ap.av.getAlignment().addAnnotation(newAnnotation); - ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0); - fullRepaint = true; + editLabelDescription(newAnnotation, true); } - else if (evt.getActionCommand().equals(EDITNAME)) + else if (EDITNAME.equals(action)) { - String name = aa[selectedRow].label; - editLabelDescription(aa[selectedRow]); - if (!name.equalsIgnoreCase(aa[selectedRow].label)) - { - fullRepaint = true; - } + /* + * non-returning dialog + */ + editLabelDescription(aa[selectedRow], false); } - else if (evt.getActionCommand().equals(HIDE)) + else if (HIDE.equals(action)) { aa[selectedRow].visible = false; } - else if (evt.getActionCommand().equals(DELETE)) + else if (DELETE.equals(action)) { ap.av.getAlignment().deleteAnnotation(aa[selectedRow]); ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]); - fullRepaint = true; } - else if (evt.getActionCommand().equals(SHOWALL)) + else if (SHOWALL.equals(action)) { for (int i = 0; i < aa.length; i++) { @@ -251,13 +251,12 @@ public class AnnotationLabels extends JPanel aa[i].visible = true; } } - fullRepaint = true; } - else if (evt.getActionCommand().equals(OUTPUT_TEXT)) + else if (OUTPUT_TEXT.equals(action)) { new AnnotationExporter(ap).exportAnnotation(aa[selectedRow]); } - else if (evt.getActionCommand().equals(COPYCONS_SEQ)) + else if (COPYCONS_SEQ.equals(action)) { SequenceI cons = null; if (aa[selectedRow].groupRef != null) @@ -272,46 +271,49 @@ public class AnnotationLabels extends JPanel { copy_annotseqtoclipboard(cons); } - } - else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE)) + else if (TOGGLE_LABELSCALE.equals(action)) { aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; } - ap.refresh(fullRepaint); - + ap.refresh(true); } /** - * DOCUMENT ME! + * Shows a dialog where the annotation name and description may be edited. If + * parameter addNew is true, then on confirmation, a new AlignmentAnnotation + * is added, else an existing annotation is updated. * - * @param e - * DOCUMENT ME! + * @param annotation + * @param addNew */ - boolean editLabelDescription(AlignmentAnnotation annotation) + void editLabelDescription(AlignmentAnnotation annotation, boolean addNew) { - // TODO i18n + String name = MessageManager.getString("label.annotation_name"); + String description = MessageManager + .getString("label.annotation_description"); + String title = MessageManager + .getString("label.edit_annotation_name_description"); EditNameDialog dialog = new EditNameDialog(annotation.label, - annotation.description, " Annotation Name ", - "Annotation Description ", "Edit Annotation Name/Description", - ap.alignFrame); + annotation.description, name, description); - if (!dialog.accept) - { - return false; - } - - annotation.label = dialog.getName(); - - String text = dialog.getDescription(); - if (text != null && text.length() == 0) - { - text = null; - } - annotation.description = text; - - return true; + dialog.showDialog(ap.alignFrame, title, () -> { + annotation.label = dialog.getName(); + String text = dialog.getDescription(); + if (text != null && text.length() == 0) + { + text = null; + } + annotation.description = text; + if (addNew) + { + ap.av.getAlignment().addAnnotation(annotation); + ap.av.getAlignment().setAnnotationIndex(annotation, 0); + } + ap.refresh(true); + return null; + }); } @Override @@ -420,6 +422,31 @@ public class AnnotationLabels extends JPanel consclipbrd.addActionListener(this); pop.add(consclipbrd); } + if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP + && PAEContactMatrix.PAEMATRIX + .equals(aa[selectedRow].getCalcId())) + { + final PAEContactMatrix cm = (PAEContactMatrix) av + .getContactMatrix(aa[selectedRow]); + if (cm != null && cm.hasTree()) + { + item = new JMenuItem("Show Tree for Matrix"); + item.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + + ap.alignFrame.showContactMapTree(aa[selectedRow], cm); + + } + }); + pop.addSeparator(); + pop.add(item); + } + + } } pop.show(this, evt.getX(), evt.getY()); } @@ -436,8 +463,7 @@ public class AnnotationLabels extends JPanel * @param pop */ static void addConsensusMenuOptions(AlignmentPanel ap, - AlignmentAnnotation ann, - JPopupMenu pop) + AlignmentAnnotation ann, JPopupMenu pop) { pop.addSeparator(); @@ -754,12 +780,12 @@ public class AnnotationLabels extends JPanel // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature // tooltips String desc = aa.getDescription(true).trim(); - if (!desc.toLowerCase().startsWith(HTML_START_TAG)) + if (!desc.toLowerCase(Locale.ROOT).startsWith(HTML_START_TAG)) { tooltip.append(HTML_START_TAG); desc = desc.replace("<", "<"); } - else if (desc.toLowerCase().endsWith(HTML_END_TAG)) + else if (desc.toLowerCase(Locale.ROOT).endsWith(HTML_END_TAG)) { desc = desc.substring(0, desc.length() - HTML_END_TAG.length()); } @@ -802,12 +828,13 @@ public class AnnotationLabels extends JPanel protected void showOrHideAdjuster(MouseEvent evt) { boolean was = resizePanel; - resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT && evt.getX() < HEIGHT_ADJUSTER_WIDTH; + resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT + && evt.getX() < HEIGHT_ADJUSTER_WIDTH; if (resizePanel != was) { - setCursor(Cursor.getPredefinedCursor( - resizePanel ? Cursor.S_RESIZE_CURSOR + setCursor(Cursor + .getPredefinedCursor(resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR)); repaint(); } @@ -1059,7 +1086,8 @@ public class AnnotationLabels extends JPanel g.translate(0, getScrollOffset()); g.setColor(Color.black); - + SequenceI lastSeqRef = null; + String lastLabel = null; AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); int fontHeight = g.getFont().getSize(); int y = 0; @@ -1084,6 +1112,7 @@ public class AnnotationLabels extends JPanel { hasHiddenRows = false; int olY = 0; + int nexAA = 0; for (int i = 0; i < aa.length; i++) { visible = true; @@ -1093,6 +1122,10 @@ public class AnnotationLabels extends JPanel continue; } olY = y; + // look ahead to next annotation + for (nexAA = i + 1; nexAA < aa.length + && !aa[nexAA].visible; nexAA++) + ; y += aa[i].height; if (clip) { @@ -1138,8 +1171,40 @@ public class AnnotationLabels extends JPanel { offset += fm.getDescent(); } - - x = width - fm.stringWidth(aa[i].label) - 3; + String label = aa[i].label; + boolean vertBar = false; + if ((lastLabel != null && lastLabel.equals(label))) + { + label = aa[i].description; + } + else + { + if (nexAA < aa.length && label.equals(aa[nexAA].label)) // && + // aa[nexY].sequenceRef==aa[i].sequenceRef) + { + lastLabel = label; + // next label is the same as this label + label = aa[i].description; + } + else + { + lastLabel = label; + } + } + if (aa[i].sequenceRef != null) + { + if (aa[i].sequenceRef != lastSeqRef) + { + label = aa[i].sequenceRef.getName() + " " + label; + // TODO record relationship between sequence and this annotation and + // display it here + } + else + { + vertBar = true; + } + } + x = width - fm.stringWidth(label) - 3; if (aa[i].graphGroup > -1) { @@ -1207,16 +1272,27 @@ public class AnnotationLabels extends JPanel } else { - g.drawString(aa[i].label, x, y + offset); + if (vertBar) + { + g.drawLine(width - 3, y + offset - fontHeight, width - 3, + (int) (y - 1.5 * aa[i].height - offset - fontHeight)); + // g.drawLine(20, y + offset, x - 20, y + offset); + + } + g.drawString(label, x, y + offset); } + lastSeqRef = aa[i].sequenceRef; } } if (!resizePanel && dragEvent != null && aa != null) { g.setColor(Color.lightGray); - g.drawString(aa[selectedRow].label, dragEvent.getX(), - dragEvent.getY() - getScrollOffset()); + g.drawString( + (aa[selectedRow].sequenceRef == null ? "" + : aa[selectedRow].sequenceRef.getName()) + + aa[selectedRow].label, + dragEvent.getX(), dragEvent.getY() - getScrollOffset()); } if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))